Summary Manhattan plots

Interaction test

Interaction test loci
index_var chr pos P_int G-W interaction effect P_joint P_marginal
rs12136785 1 89478687 4.7e-06 FALSE 6.70e-06 0.0884292
rs75242550 2 47777458 9.6e-06 FALSE 3.74e-05 0.4243720
rs12197749 6 146536288 3.1e-06 FALSE 1.92e-05 0.3766780
7:7343876_CA_C 7 7343876 2.4e-06 FALSE 7.80e-06 0.3709310
rs4128327 8 110032847 3.4e-06 FALSE 1.12e-05 0.0793897
rs555728622 10 100281893 5.8e-06 FALSE 2.62e-05 0.8744820
11:6801573_CAAA_C 11 6801573 9.1e-06 FALSE 5.60e-06 0.1917850
rs61944504 13 27321494 2.3e-06 FALSE 1.14e-05 0.3039250
rs4793425 17 70299527 2.9e-06 FALSE 8.40e-06 0.8687370
rs55690660 17 72352686 6.5e-06 FALSE 3.83e-05 0.5641650
rs1053744 22 50885775 6.1e-06 FALSE 1.33e-05 0.1111860

Joint test

Joint test loci
index_var chr pos P Genome-wide joint locus Genome-wide marginal locus
rs12727804 1 91733994 0 TRUE TRUE
rs17544265 1 215152131 0 TRUE FALSE
rs1491690 3 70131341 0 TRUE FALSE
rs4435599 10 42390234 0 TRUE FALSE
rs190316617 11 1797388 0 TRUE TRUE
rs148035207 16 6330954 0 TRUE FALSE
rs73157943 22 25333267 0 TRUE FALSE

Summarization report parameters
Parameter Value
chromosome_col CHR
position_col POS
ref_allele_col Non_Effect_Allele
alt_allele_col Effect_Allele
allele_freq_col AF
beta_interaction_col Beta_Interaction_1
p_interaction_col P_Value_Interaction
p_joint_col P_Value_Joint
p_marginal_col P_Value_Marginal
gw_threshold 5e-8
prune_threshold_int 1e-5
prune_threshold_joint 5e-8
prune_locus_width 500000
GEM_file sex_int_res_full
variant_id_col RSID
maf_filter 0.05